Papers by Neelesh Patankar
Scientific Reports, 2015
is on roughness peaks, while the roughness valleys are filled with gas. Mechanisms that 1" "
Journal of computational physics, 2015
Esophageal transport is a physiological process that mechanically transports an ingested food bol... more Esophageal transport is a physiological process that mechanically transports an ingested food bolus from the pharynx to the stomach via the esophagus, a multilayered muscular tube. This process involves interactions between the bolus, the esophagus, and the neurally coordinated activation of the esophageal muscles. In this work, we use an immersed boundary (IB) approach to simulate peristaltic transport in the esophagus. The bolus is treated as a viscous fluid that is actively transported by the muscular esophagus, and the esophagus is modeled as an actively contracting, fiber-reinforced tube. Before considering the full model of the esophagus, however, we first consider a standard benchmark problem of flow past a cylinder. Next a simplified version of our model is verified by comparison to an analytic solution to the tube dilation problem. Finally, three different complex models of the multi-layered esophagus, which differ in their activation patterns and the layouts of the mucosal...
PLOS Biology, 2015
Examples of animals evolving similar traits despite the absence of that trait in the last common ... more Examples of animals evolving similar traits despite the absence of that trait in the last common ancestor, such as the wing and camera-type lens eye in vertebrates and invertebrates, are called cases of convergent evolution. Instances of convergent evolution of locomotory patterns that quantitatively agree with the mechanically optimal solution are very rare. Here, we show that, with respect to a very diverse group of aquatic animals, a mechanically optimal method of swimming with elongated fins has evolved independently at least eight times in both vertebrate and invertebrate swimmers across three different phyla. Specifically, if we take the length of an undulation along an animal's fin during swimming and divide it by the mean amplitude of undulations along the fin length, the result is consistently around twenty. We call this value the optimal specific wavelength (OSW). We show that the OSW maximizes the force generated by the body, which also maximizes swimming speed. We hypothesize a mechanical basis for this optimality and suggest reasons for its repeated emergence through evolution.
Fluid Mechanics and Its Applications, 2006
Abstract. In the paper a Direct Numerical Simulation (DNS) scheme, named Fluctuating Immersed MAT... more Abstract. In the paper a Direct Numerical Simulation (DNS) scheme, named Fluctuating Immersed MATerial (FIMAT) dynamics, for the Brownian motion of particles is presented. In this approach the thermal fluctuations are included in the fluid equations via random stress terms. ...
Nature: Scientific reports, 2014
Nature: Scientific reports, 2014
Proceedings of the National Academy of Sciences, 2008
We report nanofabrication of protein dot and line patterns using a nanofountain atomic force micr... more We report nanofabrication of protein dot and line patterns using a nanofountain atomic force microscopy probe (NFP). Biomolecules are continuously fed in solution through an integrated microfluidic system, and deposited directly onto a substrate. Deposition is controlled by application of an electric potential of appropriate sign and magnitude between the probe reservoir and substrate. Submicron dot and line molecular patterns were generated with resolution that depended on the magnitude of the applied voltage, dwell time, and writing speed. By using an energetic argument and a Kelvin condensation model, the quasi-equilibrium liquid-air interface at the probe tip was determined. The analysis revealed the origin of the need for electric fields in achieving protein transport to the substrate and confirmed experimental observations suggesting that pattern resolution is controlled by tip sharpness and not overall probe aperture. As such, the NFP combines the highresolution of dip-pen nanolithography with the efficient continuous liquid feeding of micropipettes while allowing scalability to 1and 2D probe arrays for high throughput.
Physical Review Letters, 2008
There are contradictory published data on the behavior of fluid slip at high shear rates. Using t... more There are contradictory published data on the behavior of fluid slip at high shear rates. Using three methodologies (molecular dynamics simulations, an analytical theory of slip, and a Navier-Stokes-based calculation) covering a range of fluids (bead-spring liquids, polymer solutions, and ideal gas flows) we show that as shear rate increases, the amount of slip, as measured by the slip length, asymptotes to a constant value. The results clarify the molecular mechanics of how slip occurs. Furthermore, they indicate that in this limit, molecular dynamics simulations must accurately account for heat transfer to the solid.
Journal of Fluid Mechanics, 2010
Journal of Computational Physics, 2009
We present a computational algorithm for fully resolved numerical simulation (FRS) of rigid and d... more We present a computational algorithm for fully resolved numerical simulation (FRS) of rigid and deforming bodies moving in fluids. Given the deformation of the body in its own reference frame, the method solves for the swimming velocity of the body together with the surrounding flow field, and the hydrodynamic forces on the body. We provide the mathematical foundation of the
Journal of Computational Physics, 2009
... A numerical method for fully resolved simulation (FRS) of rigid particleflow interactions in... more ... A numerical method for fully resolved simulation (FRS) of rigid particleflow interactions in complex flows. Sourabh V. Apte a , Corresponding Author Contact Information , E-mail The Corresponding Author , Mathieu Martin a and Neelesh A. Patankar b. ... Patankar et al. ...
Journal of Computational Physics, 2004
In this paper, we present a direct numerical simulation scheme for the Brownian motion of particl... more In this paper, we present a direct numerical simulation scheme for the Brownian motion of particles. In this approach, the thermal fluctuations are included in the fluid equations via random stress terms. Solving the fluctuating hydrodynamic equations coupled with the particle equations of motion result in the Brownian motion of the particles. There is no need to add a random force term in the particle equations. The particles acquire random motion through the hydrodynamic force acting on its surface from the surrounding fluctuating fluid. The random stress in the fluid equations are easy to calculate unlike the random terms in the conventional Brownian dynamics type approaches. We present a three-dimensional implementation along with validation.
Journal of Colloid and Interface Science, 2005
Surface roughness amplifies the water-repellency of hydrophobic materials. If the roughness geome... more Surface roughness amplifies the water-repellency of hydrophobic materials. If the roughness geometry is, on average, isotropic then the shape of a sessile drop is almost spherical and the apparent contact angle of the drop on the rough surface is nearly uniform along the contact line. If the roughness geometry is not isotropic, e.g., parallel grooves, then the apparent contact angle is no longer uniform along the contact line. The apparent contact angles observed perpendicular and parallel to the direction of the grooves are different. A better understanding of this problem is critical in designing rough superhydrophobic surfaces. The primary objective of this work is to determine the mechanism of anisotropic wetting and to propose a methodology to quantify the apparent contact angles and the drop shape. We report a theoretical and an experimental study of wetting of surfaces with parallel groove geometry.
International Journal for Numerical Methods in Engineering, 2007
A new method is proposed for modelling the electrokinetic-induced mechanical motion of particles ... more A new method is proposed for modelling the electrokinetic-induced mechanical motion of particles in a fluid domain under an applied electric field. In this method, independent solid meshes move in a fixed background field mesh that models the fluid and the electric field. This simple strategy removes the need for expensive mesh updates. Furthermore, the reproducing kernel particle functions enable efficient coupling of various immersed deformable solids with the surrounding viscous fluid in the presence of an applied electric field. The electric force on a particle is calculated by the Maxwell stress tensor method. For the first time, three-dimensional assembly of nano/biomaterials of various geometries and electrical properties have been comprehensively studied using the new method. Simulation of the dynamic process of electro-manipulation of individual and multiple cells agrees well with experimental data. Preliminary results for selective deposition of viruses and stretching of a DNA molecule are also presented.
Langmuir : the ACS journal of surfaces and colloids, Jan 2, 2009
An extreme water-repellent surface is designed and fabricated with a hierarchical integration of ... more An extreme water-repellent surface is designed and fabricated with a hierarchical integration of nano- and microscale textures. We combined the two readily accessible etching techniques, a standard deep silicon etching, and a gas phase isotropic etching (XeF2) for the uniform formation of double roughness on a silicon surface. The fabricated synthetic surface shows the hallmarks of the Lotus effect: durable super water repellency (contact angle>173 degrees) and the sole existence of the Cassie state even with a very large spacing between roughness structures (>1:7.5). We directly demonstrate the absence of the Wenzel's or wetted state through a series of experiments. When a water droplet is squeezed or dropped on the fabricated surface, the contact angle hardly changes and the released droplet instantly springs back without remaining wetted on the surface. We also show that a ball of water droplet keeps bouncing on the surface. Furthermore, the droplet shows very small co...
ELECTROPHORESIS, 2006
Electroosmotic flow in a straight micro-channel of rectangular cross-section is computed numerica... more Electroosmotic flow in a straight micro-channel of rectangular cross-section is computed numerically for several situations where the wall zeta-potential is not constant but has a specified spatial variation. The results of the computation are compared with an earlier published asymptotic theory based on the lubrication approximation: the assumption that any axial variations take place on a long length scale compared to a characteristic channel width. The computational results are found to be in excellent agreement with the theory even when the scale of axial variations is comparable to the channel width. In the opposite limit when the wavelength of fluctuations is much shorter than the channel width, the lubrication theory fails to describe the solution either qualitatively or quantitatively. In this short wave limit the solution is well described by Ajdari's theory for electroosmotic flow between infinite parallel plates (Ajdari, A., Phys. Rev. E 1996, 53, 4996-5005.) The infinitely thin electric double layer limit is assumed in the theory as well as in the simulation.
Computer Methods in Applied Mechanics and Engineering, 2006
This paper summarizes the newly developed immersed finite element method (IFEM) and its applicati... more This paper summarizes the newly developed immersed finite element method (IFEM) and its applications to the modeling of biological systems. This work was inspired by the pioneering work of Professor T.J.R. Hughes in solving fluid-structure interaction problems. In IFEM, a Lagrangian solid mesh moves on top of a background Eulerian fluid mesh which spans the entire computational domain. Hence, mesh generation is greatly simplified. Moreover, both fluid and solid domains are modeled with the finite element method and the continuity between the fluid and solid subdomains is enforced via the interpolation of the velocities and the distribution of the forces with the reproducing Kernel particle method (RKPM) delta function. The proposed method is used to study the fluid-structure interaction problems encountered in human cardiovascular systems. Currently, the heart modeling is being constructed and the deployment process of an angioplasty stent has been simulated. Some preliminary results on monocyte and platelet deposition are presented. Blood rheology, in particular, the shear-rate dependent de-aggregation of red blood cell (RBC) clusters and the transport of deformable cells, are modeled. Furthermore, IFEM is combined with electrokinetics to study the mechanisms of nano/bio filament assembly for the understanding of cell motility.
Computer Methods in Applied Mechanics and Engineering, 2006
Computer Methods in Applied Mechanics and Engineering, 2010
We present a computational approach for fully resolved simulation of self-propulsion of organisms... more We present a computational approach for fully resolved simulation of self-propulsion of organisms through a fluid. A new implicit iterative algorithm is developed that solves for the swimming velocities of the organism with prescribed deformation kinematics. A solution for the surrounding flow field is also obtained. This approach uses a constraint-based formulation of the problem of self-propulsion developed by Shirgaonkar et al. . The approach in this paper is unlike the previous work [1] where a fractional time stepping scheme was used. Fractional time stepping schemes, while efficient for moderate to high Reynolds number problems, are not suitable for zero or low Reynolds number problems where the inertia term in the governing equation is absent or negligible. In such cases the implicit iterative algorithm presented here is more appropriate. We validate the method by simulating self-propulsion of bacterial flagellum, jellyfish (Aurelia aurita), and larval zebrafish (Danio rerio). Comparison of the computational results with theoretical and experimental results for the test cases is found to be very good.
Computer Methods in Applied Mechanics and Engineering, 2005
In this paper we present a distributed lagrange multiplier (DLM) based Stokes flow algorithm for ... more In this paper we present a distributed lagrange multiplier (DLM) based Stokes flow algorithm for particulate flows. The entire fluidparticle domain is treated as a fluid. The fluid in the particle domain is ensured to move rigidly by adding a rigidity constraint. We modify the SIMPLER ...
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Papers by Neelesh Patankar